Protein structure prediction is an important problem in the post-genome era, which is one possible way to fill the gap between the rapid-growth sequences and the relative small number of proteins with experimentally determined structures. Despite the structural genomics initiatives and biochemical efforts, the cheapest and fastest way to obtain structural information is through prediction algorithms. Structure prediction, even in the absence of homology, is the first step of the sequence-structure-function paradigm. Great progress has been achieved in protein structure prediction during the last decades. The development of high-quality prediction methods has also been boosted by objective community-wide assessment experiments. However, the ultimate goal of protein structure prediction remains far away to reach. New algorithms, theory and advanced prediction techniques are necessary to facilitate the progress. With this special issue of International Journal of Data Mining and Bioinformatics, we wish to explore the state of the art in protein structure prediction, identify what progress has been made, and highlight where future effort may be most productively focused. The topics of interest include, but are not limited to:

Important DatesSubmission of abstracts: June 15, 2009Submission of manuscripts: June 30, 2009Author notification: August 31, 2009Revised versions due: September 30, 2009Second review back to the authors: October 31, 2009Final manuscripts: November 30, 2009Paper publishing: 2010